MolNFT v1 · #128384 · protein
Structure of truncated norcoclaurine synthase from thalictrum flavum with product mimic
5NON · S-norcoclaurine synthase: “Structure of truncated norcoclaurine synthase from thalictrum flavum with product mimic”. X-ray diffraction, 1 ligand (93H), 6 pockets (best druggability 0.73). MolNFT v1 #128384 on GenesisL1: 3D…
- PDB
- 5NON
- Type
- protein
- Length
- 470 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-norcoclaurine synthase
- EC
- 4.2.1.78
- UniProt
- Q67A25
- Ligands
- 93H
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-norcoclaurine synthase (EC 4.2.1.78) | protein | 155 | 25% helix, 45% strand | Q67A25 |
| B | S-norcoclaurine synthase (EC 4.2.1.78) | protein | 158 | 26% helix, 44% strand | Q67A25 |
| C | S-norcoclaurine synthase (EC 4.2.1.78) | protein | 157 | 27% helix, 44% strand | Q67A25 |
Ligands and binding sites
- 93H · 4-[2-[2-(4-methoxyphenyl)ethylamino]ethyl]benzene-1,2-diol · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.73 | 0.86 | 32 | 93H |
| 2 | 283 | 0.73 | 0.86 | 33 | 93H |
| 3 | 268 | 0.71 | 0.85 | 30 | 93H |
| 4 | 607 | 0.67 | 0.77 | 63 | empty |
| 5 | 82 | 0.40 | 0.78 | 19 | empty |
Interfaces
2 interfaces between chains.
- B–C · 651 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 599 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5NON · Structure of truncated Norcoclaurine Synthase from Thalictrum flavum with product mimic · the same entry in another collection · chain A against A, TM-score 1.00
- Q67A25 · AlphaFold monomer V2.0 prediction for S-norcoclaurine synthase (Q67A25) · a predicted model of the same protein · chain C against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q67A25
- Elsewhere: RCSB PDB 5NON · PDBe 5NON · UniProt Q67A25
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